There are several unseen things that can affect song volume (sic) - there is, technically speaking, no such thing because volume is the analog output of sound, and as we all know, MIDI is not sound. Technically, the volume of playback is determined by the tone engine designated to decode the MIDI messages. It can take commands from the settings you make for the Part designated to decode the data. It can take messages from connected, assigned controllers. And/or It can also take commands from messages in the track data itself.

If there are messages in the track data (unseen) you will need to edit that message.
_ cc007 is the Main channel Volume, if such a message is in the track data it will cause the slider icons to animate on the Montage (the red light indicator next to the Fader and the slider screen graphic will reflect the change in channel volume).
_ cc011 is Expression, it too can affect the relative volume of the Part. An FC7 pedal plugged into Foot Controller 1 will default to Expression. And unless stored otherwise in the track, the default is 127 for Expression. But not to worry, cc011 set to 127 will never exceed the the setting for the Main channel Volume (cc007).

In other words, if you set the Main channel Volume to 96, your screen slider will indicate "96" (cc007), this means the toe-down position of Expression pedal maxes out at "96". Expression (cc011) always works within the limit of Main channel Volume (cc007).

The other unseen wild cards include the Super Knob or any assigned parameter that is set to directly influence the Part's Volume output.

How to proceed to figure this out:
Check the stored volume setting for the Part, or Parts, in question. You can do so by recalling the Performance (move away and come back)
Observe the exact Main channel Volume for each Part in question. The Main channel Volume for each Part is stored in the Performance.
Start your .mid file and see if these value change when you start the file.
This will tell us if the stored values agree with what's written into your file.

Let us know.

No luck. I saved it as a midi file so I could look at it in an external sequencer. There were no controller messages in the file so I added a cc007 at 80 then brought it back into montage.

The level for the part in question happens to be saved as 88. When I press play and then load the midi file and press play again the level indicator for the part changes to 80 but the output is definitely higher than 80. If I press play again the level sounds like what I would expect 80 to be when compared to the other parts present. It can't be a super knob issue as the performance was created from an Init so there was no "legacy" info present.

To be clear, so I'm understanding the issue... You store this Part, Part "X" at a volume of 88.
When you recall this program the volume reads 88, but the volume when select and play this Part is actually much louder than the 88 setting should be (compared to the other Parts)

You start playback of the file, cc007 sets the Part's volume as expected to the 80 value that input into the track data (cc007 = 80).
And still the Part is playing at full volume... Is this correct?

Is there any other information that we're missing, any Sysex data in the track, any external device connected, etc.?

What Part number are we dealing with?
Is this a Part you copied/merged or is it one you made yourself?

That's nearly correct. When the part is played on its own the volume is what would be expected but when the file plays back (though only the first time) the volume is louder than the 80 shown.

It is in Part 6 and is merged from another performance which itself was a part that I created from scratch.

I'm wondering if I'm doing something wrong when I recorded the song and then loaded it in later - what should the procedure for that be?

It is in Part 6 and is merged from another performance which itself was a part that I created from scratch.

? Not sure what to make of that... Guess I have to ask what do you have assigned to control VOLUME within this Part. As I mentioned there are unseen controls that can influence the output level of a sound.
Press [EDIT]
Select the Part 6
Look at its "Mod/Control" > "Control Assign" box
Set the Display Filter to "All"
Review the different PAGES of assignments looking for something that is assigned to Volume or affects volume

I'm wondering if I'm doing something wrong when I recorded the song and then loaded it in later - what should the procedure for that be?

Where did you record the Song?

The song was recorded on the montage itself.

When I've entered the edit page for Part 6 and then Mod/Control Control Assign there are 2 pages but there is no mention of anything volume related just Cut Off (Mod Wheel) and Coarse (Assign Sw2)

I'm baffled.

i love a mystery.

Once you have edited your Performance, you should Store it, renaming it when offered (very important) so that it takes a place in your USER area that has a different name from wherever you started.
Once you recorded the Song -the song is placed in your Song folder. Give the Song a name by touching the default name and selecting "Rename"

Start playback to ensure you have the right Performance and Song combination.
Make sure the Volumes of all Parts are set where you want them
Press [STORE]
You will "Overwrite Current Performance"
This should link the "Song&Perf" so that any time you touch the SONG NAME area and select "Load" you are taken to "Song&Perf" and when you load your data it should recall the exact condition you desire.

Let us know.

I'll give that a go over the weekend and keep you posted on the progress - many thanks for the help so far

I think I've got it. I tried it with a simple example first and then using the performance I would be requiring it with. It was only then that I realised where the rogue midi data was coming from - my foot was on the FC7 pedal so it was recording my movements so no wonder it was at full volume as it had it in toe down position. I only realised this when one of my examples suddenly increased in volume part way through.